Tuesday, February 28, 2012

(Note: I’m publishing this post concurrently with my blog bud Chemjobber. Hop on over to his site to read about the industry / academia training and #chemjobs angles. This way, regular readers get twice the opinions for half the price!)

Who wants to chat?
Source: Texas A&M U.

As 2011 drew to a close, John Gladysz, the new Chief Editor of Organometallics, sat down for a chat with seventeen organometallic chemists from different national (German, Swiss, Australian, US, Chinese, British) and employment backgrounds (14 academia, 2 industrial, 1 government). The result? An in-depth discussion, full of banter and back-talk, which covers topics such as industrial training for grad students, national creativity differences, “dream reactions,” and how to encourage industrial cross-collaboration.

As an icebreaker, Gladysz had each chemist dream up their “Christmas Stocking Reaction,” the ultimate goal each would love to see realized. Here’s a quick rundown:

-Pragmatism –Joachim Ritter (DuPont) envisioned several scenarios for taking non-petroleum-derived feedstocks on to commodity chemicals. Ritter’s focus on hydroxymethyl-furfural (HMF, a darling of ChemEng labs across the country) was perhaps unsurprising, but I enjoyed his new ideas for deoxygenation of vegetable oils to produce fine chemicals. Jerzy Klosin (Dow) chimed in for development of newer, cheaper catalytic complexes, especially championing first-row analogues for replacement of palladium in polymerizations. Bernhard Rieger (Technische U. Munschen) weighed in on incorporation of CO2 into polymers with nickel catalysts.

-Mind your MOFs – Still others, such as Zach Ball (Rice U.) and Ekkehardt Hahn (Westfalische Wilhelms-Universitat Munster) weighed in on new types of building blocks and metals for cluster and MOF chemistry. Vivian Yam (U. of Hong Kong) wrapped up everyone’s requests with a nice bow; she hoped for new air- and moisture-insensitive OLED materials, solar energy-collecting polymers, and water-splitting photocatalysts.

Filling the “Tool Box” - Rieger cautioned to watch out for the recurring industrial opinion that “all the useful chemistry is already discovered.” Gladysz used the example of frustrated Lewis pairs, which, while a fairly young concept, are already turning heads. Bill Jones gave an impromptu one-liner about heterolytic hydrogenation: “If someone had written that on an exam…you’d give them a zero (back in the old days).” Humphrey chimed in on bimetallic bases, and Klosin for Ziegler-Natta studies.

But just then, Ritter poured cold water on the party: “Today’s chemical companies are busy reacting to rapid market swings and trends, which does not leave a lot of room for risky long-term projects.” Sensing, perhaps, that he’d deflated the roundtable’s enthusiasm, he quickly backtracked and mentioned that he’s “looking forward to…CO2 utilization, solar energy, and biomass based energy and chemicals.”

So there you go, future faculty members, he’s written half your proposal already!

Throwaway lines – CJ has collected quite a few of these, but I’d like to comment on a few more.

“I’ve talked to a colleague in China whose professor advised ‘If you don’t do palladium chemistry, how will people know you are my student?’.” –Vy Dong

Peering into the OM "xstal ball "
Source: Organometallics

This issue seems to rankle most with the faculty, who toe the fine line between capitalizing on their past successes and striking out with their own programs. Suzanne Blum (UC-Irvine) cautioned against what she calls “n+1 research,” clinging to well-trodden paths while writing funding proposals. But Yam and Humphrey pointed out that initial funding in their home countries (China, Australia) can be tough unless you stick to the script.

This creativity discussion wound through the group, until Yam and Hahn debated whether Indian and Chinese universities still seemed to hire based on quantity (i.e. papers published) vs. quality.

Hahn: “…even the 28-year old researchers from China know their h-indexes [and] introduce themselves saying their name and ‘I have an h-index of 10.’ And you wonder who has trained them?”

I can’t say that I’ve never encountered the "publish or die" sentiment, but I had hoped it was becoming less prevalent with time. Readers, your thoughts?

The Last Word - “…in my opinion, the chemical community performs poorly in transmitting to the general public what they are actually doing.” –Ekke relays a sobering thought for those of us in the blogosphere who toil daily to demystify our science.

Monday, February 27, 2012

On a recent visit to a major US university, I had occasion to stop outside the towering steel gates leading into the main courtyard of the newly-constructed chemistry building. I glanced up, and saw organic molecules, decked out in bronze, blue, and red.

On either side of the gate are polypeptides, four residues each, that use standard amino acid abbreviations to spell out a four-letter word* on either side. Pictured (at left) is the left-hand gate.

He's the director of the Hayden Planetarium. He's appeared on The Colbert Report, The Daily Show, and Late Night with Conan O'Brien. He answers astronomy questions posed to him by random netizens on reddit, and gives dozens of public talks to school kids.

Noted science writer Carl Zimmer has recently written a fairly glowing profile of him, that appeared in a well-read magazine.

He hosts episodes of NOVAfor PBS, and Fox will re-boot Cosmos with him in front.

But it was his AP stock photo (see right) from this NPR book review that drew my eye - when's the last time being a scientist looked socool?

Saturday, February 25, 2012

Natural product isolation chemists find fascinating molecules in wild, unexpected places. Hippo sweat. Deep-sea hydrothermal vents. Horse urine. Even maple syrup refining produces new compounds that chemists hope could be the next wonder drug. But a new paper from Org. Lett. ASAP brings forth a new discovery arena for me: dung beetles. Specifically, the giant balls of, well . . .poop, that they push around, then lay their eggs in.

Dung beetles with brood ball

Korean researchers have isolated tripartilactam from a Streptomyces species living in the beetles' brood ball, which they broke apart, cultured, and fractionated. Although the compound has no real biological activity, look at that structure: an 18-4-8 tricycle! Now, cyclobutanes are found in natural products all the time, from sceptrin to ladderanes, but usually not as a "bow-tie" bringing together two huge macrocycles. These scientists figure that a larger polyunsaturated structure was knit together by bacterial enzymes called polyketide synthases, followed by a light-initiated [2+2] to snap the cyclobutane shut.

Chemistry Note: Did you see that 18-4 trans ring juncture? Normally, that species would be far too strained to exist in anything below an 8-4 system. However, in a ring as large as 18, even with the rigid geometry enforced by the lactam and polyolefin chain, there's still enough wiggle room to accomodate this odd duck.

Back in Junior High School1, my first chemistry teacher ran a fascinating experiment. He dabbed a small amount of dilute capsaicin on the back of a piece of bread, and handed it to each class member. Of course, most of us felt the burn, but not one girl - she was genetically insensitive to capsaicin’s painful effects.

The science of taste and smell fascinate me, since they not only underlie many of our daily chemical interactions, but provide clear survival benefit to the species. The ability to smell smoke or taste bitter alkaloids might allow you to detect fires or avoid poisonous foods. In 2006, Glindemann and coworkers reported the source of the “iron smell,” the dark, musky odor produced when you touch coins or metal handles. His group traced the smell back not to compounds in the metal itself, but to chemical changes of body oils spontaneously produced upon contact (one of the stronger odorants, 1-octen-3-one, shown at left). The chemists theorize that the ability to smell these metallic odors traces far back in our evolutionary history, to when “blood smell” helped early human hunters track their prey through the woods.

Well, if smells are so critical, pity the poor astronauts. Space missions show that after a few days in weightless conditions, astronauts can no longer smell or taste their food properly, and begin to crave hot spices and bold flavors. NPR reporter Joe Palca explored this condition, called “stuffy-nose effect” or the “Charlie Brown syndrome” (due to the enlarged appearance of your head in space when your facial tissues swell with fluid, an effect of lessened gravity).

Charlie Brown and Snoopy
Source: The Telegraph | Charles M. Schultz

Want to help test the phenomenon? A joint Cornell /U.Hawaii study is now recruiting applicants. You’ll live in a simulated Mars mission habitat in Hawaii, where researchers will test food preparation with limited ingredients. They’ll induce the “stuffy-nose effect” with specialized beds that keep the head slightly lower than the rest of the body, and test various spices and food replacements for space palatability.

Maybe these scientists shouldn’t worry about smell deprivation, and just recruit a bunch of supertasters. These genetically gifted sense superstars possess more taste buds (papillae) on the tongue surface than others, which can be observed by simply staining the tongue blue and looking in a mirror. Supertasters report heightened sensitivity to subtle changes in food or drink, and naturally cluster in occupations such as chefs or sommeliers.

Count the taste buds!
Source: NPR | Maggie Starbard

The physiological prowess of supertasters was first noted in back-to-back PNAS papers in the 1930s. Amazingly, the trend started when two chemists – Drs. Fox and Noller, of DuPont – exhibited markedly different reactions to the taste of phenyl thiocarbamide dust in the air. The two scientists then prepared several analogues of the parent thiocarbamide, and ran around asking people to taste them!

The second paper, from geneticist Albert Blakeslee at the Carnegie Institution in Cold Spring Harbor, tested the effect of dilution on the taste sensations of a few hundred people of different racial and ethnic backgrounds. On the menu, in addition to the DuPont compound, were hydrochloric acid, picric acid, salt, and saccharine. Blakeslee found that there were distinct groups of people who could taste at certain thresholds, the “tasters” and the “non-tasters.” Further research, as explained by food scientist John Hayes in a broadcast of the WNPR Colin McEnroe show a few nights back, has shown that humans actually fit into three distinct categories: “non-tasters,” “medium-tasters,” and “supertasters.” The updated test involves placing a small crystal of propylthiouracil (PTU, see above) on the tongue and recording the intensity of the each person’s reaction; supertasters recoil at the bitterness, while “non-tasters” barely notice a difference.

1.No, it wasn’t ‘middle school’ back then, and yes, I walked uphill both ways, in the snow, carrying my books.

Yup. Biologists love a good play on words. Among the well-known Drosophila (fruit fly) genes are lush, sonic hedgehog, and methuselah*. In our bodies, certain drugs interact with the hERG receptor, one of several human homologues (close matches) to fly genes. But I hadn't realized that this PK point of conversation was named for a night club in L.A.

Ever heard of a "go-go" dancer?

Urban legend holds that famed club Whisky a Go-Go, a 1960s rock music hotbed, first institutionalized the profession when it opened on the Los Angeles Sunset Strip. To capitalize on a popular trend from New York and Paris, the owners set girls to "go-go" dancing in large cages suspended from the ceiling.

Not a Drosophila geneticist.

What's "go-go" dancing, you ask? Think of the female silhouettes you see before movies like James Bond, or better yet later spoof Austin Powers: International Man of Mystery - Tall boots, short skirts, and lots of hip shakes and leg twists. So, what does this have to do with fruit flies, or human drug testing?

As recounted in a 1991 Science Newsfeature, neurogeneticist William Kaplan first noted the ether-à-go-go (eag) mutation in the 1960s. If these flies were knocked out with ether, their legs would twitch and shake, much like the famed dancers. When two researchers from the University of Wisconsin discovered similar mammalian genes, they took a page from the same book, naming them "erg," or "ether-à-go-go related genes."

ECG of a single heartbeatSource: Wikipedia Commons | Agateller

Warmke and Ganetsky, the two Wisconsin geneticists, found that the hERG gene encoded specific voltage-gated potassium channels in cell membranes (i.e., they open and close to allow potassium ions to flow out of the cell). In heart cells, these channels control the back-end of the heartbeat, the so-called "QT interval" (see graphic). When drugs block these channels, cardiac membrane repolarization (electrical charge balancing) takes longer, and a fatal arrhythmia may set in.

Seldane (terfenadine)

Anyone remember Seldane (terfenadine)? In the late 1980s, allergy sufferers praised it as a non-sedating antihistamine. However, it became a hERG poster child, and the FDA recommended its removal from the market in 1997.

Saturday, February 18, 2012

Sensationalist journalism pervades our society. Usually, investigators focus their attention on stores, local government, unions, and the like. But chemistry labs...are they terrorist plots waiting to happen? Lucky for us, ChemBark to the rescue! His post Friday (click over there to see the video in all its scandal-filled and melodramatic musical glory) alerts the chemical community to a pressing National Security emergency: unlocked research labs in otherwise nondescript academic buildings.

To reiterate Paul's main point: yes, the labs in question should not have been so easy to access. Most of the academic labs I've worked in have had key card / ID fob access built into the doors, and critical facilities (storerooms, NMR, clean rooms) behind keypad-locked doors, or good old-fashioned metal lock and key.

Cogent arguments aside, the piece fails on just about every level for meaningful chemistry communication. Here's a random sampling of quotes from the story:

0:10 "...just the right chemicals to make a bomb?"
Well, most bombs require high explosives, like nitroglycerin or TNT. As most readers of this blog realize, materials such as iodine or hydrazine - unlike the dilute HCl or ethyl ether featured in the news spot - can actually be used to make bombs, and are under strict DOT and DHS purchase regulations.

0:53 - What's with the gunshots? Since when did that have anything to do with organic chemistry labs?

1:16 - "Compounds that could potentially be used in terrorist attacks"
While (potentially) true, you're more likely to find allyl alcohol in drug leads, and acrylonitrile in superglue!

2:43 - "...chemistry lab and storeroom." Have these people ever seen a chemical storeroom?

2:50 - "...cabinets, some unlocked, labeled ACIDS and FLAMMABLES."
Were the researchers supposed to just store them in plain gray cabinets? I would argue that the labels increase safety. Also, if they were allegedly "unlocked," why is there no camera shot of a cabinet door hanging open?

3:05 - "...large nitrogen tanks..." If the announcer knew that he was referring to liquid nitrogen, he'd be doubly afraid!

3:54 - "...hydrochloric acid, a highly corrosive chemical that can burn skin to the bone"
This bottle reminds me of the 1.0N HCl shown earlier (1:29). If anyone's wondering, the pH of 1N HCl is 0.1, which, while enough to give you some decent skin irritation, won't char you on contact. I see no concentrated HCl anywhere, and even that's no TFA or triflic acid.

4:07 - "...ethyl ether, a highly flammable solvent that could cause respiratory problems!"
Or knock you out for surgery, like in the olden days at the MGH Ether Dome.

6:01 - "schools must list their chemicals of interest, but only if those chemicals exceed a certain amount"
This sounds an awful lot like "the dose makes the poison." (i.e., it's terribly tough to mount a terrorist attack with 25 g of magnesium sulfate...)

**Just for those keeping score at home, I counted 26 mentions of the word "chemical" (or once every 14.4 seconds). Always preceded by a sensationalist adjective like "dangerous," "deadly," "interest," "maim," or "flammable."

Thursday, February 16, 2012

The other night, while eating at a fine American gourmet restaurant, I happened upon some "found chemistry" on a soda cup (see right).

At first, I downplayed it to sketchbook advertising gone mainstream. After thinking about it some more, though, I realized it was really a clever little doodle. Consider the Rosetta Stone, a stone version of "Hieroglyphics for Dummies" that allowed Egyptologists to begin deciphering the ancient script via Greek, which they knew.

This graphic bridges four linguistic worlds: English, Spanish, chemistry, and symbolism (see how it's drawn in the shape of a water droplet?). Naturally, I couldn't get the concept out of my head, and decided to try my hand at a few of my own.

Tuesday, February 14, 2012

If you died tomorrow, would someone continue your work?...even up to publication?

Prof. Keith Fagnou
Credit: U. of Ottawa

This thought gave me pause yesterday, as I browsed through journal contents and realized that Prof. Keith Fagnou, formerly of the University of Ottawa, was still publishing well into 2012.

For those unaware: Fagnou passed away unexpectedly in November 2009 after a short bout with H1N1 flu, only 38 years old. His research group, dubbed "The Fagnou Factory," kept coming to work, and kept publishing.

Between 2010-2012, despite Fagnou's death, he authored nearly 20 publications (and counting!). And these aren't retrospectives or reviews, but deep mechanistic and methodological studies, which landed in high-end places like Org. Syn., JACS, and Angewandte Chemie.

So what's the secret to Fagnou's seemingly eternal success?

First, it pays to work in a "hot" scientific area. In the mid 2000's, C-H activation chemistry was booming, and KF was among the vanguard. From direct Pd-catalyzed arylations of pyridine N-oxides and alkylations of perfluoroaromatics, to Rh(III) cyclizations and explorations into -OPiv metal coordination, Fagnou's research had just begun to take off.

Second, his beloved "Factory" really seemed to love him back. Over his seven-year career at Ottawa, Fagnou mentored 4 postdocs, 24 graduate students, and 22 undergrads, many of whom would later stay on with him to pursue their doctoral degrees. After Keith's death, his group members organized a symposium in his honor, and even assembled a "Chuck Norris legends"-type tribute to him, in a mock JACS template.

I briefly met with Keith after a seminar, and he told us stories of his time as a schoolteacher and hilarious blooper-reel recaps of his time in the Canadian Navy. Everyone at the table felt his enthusiasm for chemistry (and life in general) really got him out of bed in the morning, and inspired others to do the same.

Here's to continued Keith's continued success; if I see an abstract in 2020, I'll hardly be surprised.

Update (2/15/12, 7:30) - Almost forgot this mini-review, published over at Chemistry Blog about a year ago. Derek's post on Keith generated an overwhelmingly supportive row of comments.

Thursday, February 9, 2012

Last night, while reading through the Feb. 6 issue of C&EN, I found myself terribly amused by the inside back cover. The ad, for ACS journal Organometallics(*now under new management!), encouraged readers to check out their 2011 Roundtable. This panel of distinguished chemists met together last year to opine on issues ranging from new research frontiers and publication strategies to the role of basic research in developing new industrial reactions.

A hand-drawn cartoon, purportedly of chemists in concilium adorns the article. Clearly, the artist intends for this to be modern-day: laptop computers, desk chairs, and a multinational group discuss science with rapt attention.

But the picture I found so funny wasn't this one, but instead the magazine cartoon, which re-imagined the same meeting as if the chemists were members of King Arthur's court. Which got me to thinking - I've dabbled a bit in catalysis and complexes, so who would I want on my round table?

I've taken the liberty of labeling the photo with my potential knights. Readers, with whom would you want to ride into battle discuss organometallic chemistry?

Monday, February 6, 2012

It's clear that we generate neologisms nowadays simply by stitching old words together.

I'm tired of writing this sinfo on microsyn...time for skitter?

The trend has a name: portmanteau words. Attributed to wordsmith Lewis Carroll in the late 19th Century, the practice has evolved with the internet age to describe complex ideas in tiny verbal bundles. For instance, a locavore is a "local omnivore," or someone who eats foods located sourced from within a certain radius of his home.

Not that we chemists should be surprised. After all, we're responsible for many of these words, and we use them every day. The aldol reaction takes an aldehyde and an enol to forge new carbon-carbon bonds. Using small organic molecules for catalysis? Organocatalysis. Why talk about reduction and oxidation cycles, when you could just say redox?

So, in an effort to increase synthetic chemists' efficiency, I'd like to propose several new portmanteau words:

Sunday, February 5, 2012

Just in time for Super Bowl 46 (XLVI, for those playing in ancient Rome), The New York Times recently published a humorous collage of ESPN sportscasters' cliches over the past six months of NFL coverage. One tract specifically caught my eye:

Wow, two chemical terms in the same sentence! I understand, then, that Ray Rice, in addition to being a nitroglycerin-soaked fiber cylinder with a blasting cap, can also reduce kinetic barriers (tackles?) to fundamental reaction steps (gaining touchdowns, no doubt).

I can see the similarity, if I look hard enough. After all, both football and chemistry research share collisions, (grid)iron, receivers, and a love of all things statistic.

Just don't compare high "turnover numbers" (TON)...the NFL doesn't look as kindly on those as scientists do!

Friday, February 3, 2012

While flipping through the JACS ASAP abstracts, I noticed this scheme from a group in Poland. My first thought, though, was not "Oh, cool, fused* porphyrins."

Nope. Instead, I thought "The coloring bug has spread!"

Credit: ACIEE, Nicolaou group

See, for a few years now, certain organic chemists have begun to "ink" their reaction schemes. At first, the rationalization was beauty, the notion that artistic flair livened up the work. Then, the noveau artistes spoke of functionality, indicating similarly sized groups, say, or drawing the reader's eye to certain molecular features (Note: go here or here for Derek's ITP take, or here for TotSyn's)

Lately, though, it's like a child has spilled his watercolor paints all over the abstract. Maybe these guys should team up on that new ACS coloring book.

Don't get me wrong, I'm all in favor of scientific visualizations that help illustrate a concept, like the winners of the 2011 International Science and Engineering Visualization Challenge. And seminar slides with some red or blue structures never hurt anyone. But colored reaction schemes seem, to me, to be more about catching the eye (Wow, look over there!) than communicating good science.

Credit: JACS, Glorius group

Readers, what do you think? Am I just missing the point here? Or do you find the coloring-book approach equally vexing?

I look forward to a spirited debate in the comments!

*(Bonus chemistry word of the day, for those playing at home: tetrabenzochrysenoporphyrin!)

I live in a sleepy town of about 28,000 people. Quiet, picture-postcard-like scenery. A few coffee shops and pizza joints. Schoolchildren, soccer moms, and tall pine trees. The type of town where a visit to the local library might normally turn up mysteries, nonfiction, and children's books, but not a lot of science content.

So, imagine my surprise at finding a veritable treasure trove in our "New Books" section last week. As I strolled by, I couldn't help scooping up everything I laid my eyes on.

See Arr Oh

Who is this masked chemist?

Finding my way through new challenges.
I was a founding blogger at Scientific American's Food Matters and Blog Syn. I once wrote for C&EN's The Haystack. I've written for Nature Chemistry, Newscripts, Chemistry Blog, Chemjobber, and Totally Synthetic.